Difference between revisions of "Keywords"
From Phaserwiki
(→link=WAVELENGTH) |
|||
Line 16: | Line 16: | ||
*[[Image:Developer.gif|link=]] [[#Developer Keywords | Developer Keywords]] | *[[Image:Developer.gif|link=]] [[#Developer Keywords | Developer Keywords]] | ||
− | + | Phaser can be compiled as a python library | |
+ | Input is via Python functions equivalent to the keyword input | ||
+ | Phaser uses cctbx variable types | ||
'''Python variable types''' | '''Python variable types''' | ||
* Miller = cctbx::miller::index<int> | * Miller = cctbx::miller::index<int> |
Revision as of 22:28, 3 May 2012
These keywords are for the current (nightly build) release of Phaser through Phenix .
Phaser runs in different modes, which perform Phaser's different functionalities. The mode is selected with the MODE keyword. The different modes and the keywords relevant to each mode are described in Keyword Modes.
Most keywords only refer to a single parameter, and if used multiple times, the parameter will take the last value input. However, some keywords are meaningful when entered multiple times. The order may or may not be important.
Phaser can be compiled as a python library Input is via Python functions equivalent to the keyword input Phaser uses cctbx variable types Python variable types * Miller = cctbx::miller::index<int> * dvect3 = scitbx::vec3<floatType> * dmat33 = scitbx::mat3<floatType> * type_array = scitbx::af::shared<type> arrays
Basic Keywords
ATOM
- ATOM CRYSTAL <XTALID> PDB <FILENAME>
- Definition of atom positions using a pdb file.
- ATOM CRYSTAL <XTALID> HA <FILENAME>
- Definition of atom positions using a ha file (from RANTAN, MLPHARE etc.).
- ATOM CRYSTAL <XTALID> [ELEMENT|CLUSTER] <TYPE> [ORTH|FRAC] <X Y Z> OCC <OCC>
- Minimal definition of atom position. B-factor defaults to isotropic and Wilson B-factor. Use <TYPE>=TX for Ta6Br12 cluster and <TYPE>=XX for all other clusters. Scattering for cluster is spherically averaged. Coordinates of cluster compounds other than Ta6Br12 must be entered with CLUSTER keyword. Ta6Br12 coordinates are in phaser code and do not need to be given with CLUSTER keyword.
- ATOM CRYSTAL <XTALID> [ELEMENT|CLUSTER] <TYPE> [ORTH|FRAC] <X Y Z> OCC <OCC> [ ISOB <ISOB> | ANOU <HH KK LL HK HL KL> | USTAR <HH KK LL HK HL KL>] FIXX [ON|OFF] FIXO [ON|OFF] FIXB [ON|OFF] BSWAP [ON|OFF] LABEL <SITE_NAME>
- Full definition of atom position including B-factor.
- ATOM CHANGE BFACTOR WILSON [ON|OFF]
- Reset all atomic B-factors to the Wilson B-factor.
- ATOM CHANGE SCATTERER <SCATTERER>
- Reset all atomic scatterers to element (or cluster) type.
setATOM_PDB(string <XTALID>,string <FILENAME>) setATOM_HA(string <XTALID>,string <FILENAME>) addATOM(string <XTALID>,string <TYPE>,float <X>,float <Y>,float <Z>,float <OCC>) addATOM_FULL(string <XTALID>,string <TYPE>,bool <True=ORTH False=FRAC>,dvect3 <X Y Z>,float <OCC>,bool <True=ISO False=ANO>,float <ISOB>,bool <T=ANOU F=USTAR>,dmat6 <HH KK LL HK HL KL>,bool <True=FIXX False=REFX>,bool <True=FIXO False=REFO>,bool <True=FIXB False=REFB>,bool <True=SWAPB False=!SWAPB>,string <SITE_NAME>) setATOM_CHAN_BFAC_WILS(bool <True|False>) setATOM_CHAN_SCAT(string <TYPE>)
CLUSTER
- CLUSTER PDB <PDBFILE>
- Sample coordinates for a cluster compound for experimental phasing. Clusters are specified with type XX. Ta6Br12 clusters do not need to have coordinates specified as the coordinates are in the phaser code. To use Ta6Br12 clusters, specify atomtypes/clusters as TX.
setCLUS_PDB(string <PDBFILE>)
COMPOSITION
- COMPOSITION BY [AVERAGE|SOLVENT|ASU]
- Alternative ways of defining composition, by AVERAGE solvent fraction for crystals (50%), specified SOLVENT content, or explicit composition of ASU.
- COMPOSITION PERCENTAGE <SOLVENT>
- Composition entered by solvent content.
- COMPOSITION PROTEIN [ MW <MW> |SEQUENCE <FILE> | NRES <NRES> | STR <STR> ] NUMBER <NUM>
- Contribution to composition of the ASU. The number of copies NUM of molecular weight MW or SEQ given in fasta format (in a file FILE) or number of residues <NRES> or a sequence string (no spaces) of protein in the asymmetric unit.
- COMPOSITION NUCLEIC [ MW <MW> |SEQUENCE <FILE> | NRES <NRES> | STR <STR> ] NUMBER <NUM>
- Contribution to composition of the ASU. The number of copies NUM of molecular weight MW or SEQ given in fasta format (in a file FILE) or number of residues <NRES> or a sequence string (no spaces) of nucleic acid in the asymmetric unit.
- COMPOSITION ATOM <TYPE> NUMBER <NUM>
- Add NUM copies of an atom (usually a heavy atom) to the composition
- Default: COMPOSITION BY ASU
CRYSTAL
- CRYSTAL <XTALID> DATASET <WAVEID> LABIN Fpos =<F+> SIGFpos=<SIG+> Fneg=<F-> SIGFneg=<SIG->
- Columns of MTZ file to read for this (anomalous) dataset
- CRYSTAL <XTALID> DATASET <WAVEID> LABIN F =<F> SIGF=<SIGF>
- Columns of MTZ file to read for this (non-anomalous) dataset. Used for LLG completion in SAD phasing when there is no anomalous signal (single atom MR protocol). Use LABIN for MR.
ENSEMBLE
- ENSEMBLE <MODLID> PDB <PDBFILE> [RMS <RMS>|IDENTITY <ID>] {PDB <PDBFILE> [RMS <RMS>|IDENTITY <ID>] }…
- The names of the PDB files used to build the ENSEMBLE, and either the expected RMS deviation of the coordinates to the "real" structure or the percent sequence identity with the real sequence.
- ENSEMBLE <MODLID> PDB <PDBFILE> CARD ON
- The name of a (non-standard) PDB file used to build an ENSEMBLE. The RMS deviation is parsed from special REMARK cards of the pdb file (e.g. "REMARK PHASER ENSEMBLE MODEL 1 ID 31.2") containing the superimposed models concatenated in the one file. This syntax enables simple automation of the use of ensembles. The pdb file is non-standard because of the addition of information to the REMARK card and also because the atom list for the different models need not be the same.
- ENSEMBLE <MODLID> HKLIN <MTZFILE> F=<F> PHI=<PHI> EXTENT <EX EY EZ> RMS <RMS> CENTRE <CX CY CZ> PROTEIN MW <PMW> NUCLEIC MW <NMW>
- An ENSEMBLE defined from a map (via an mtz file). The molecular weight of the object the map represents is required for scaling. The effective RMS coordinate error is needed to judge how the map accuracy falls off with resolution. The extent (difference between maximum and minimum x,y,z coordinates of region containing model density) is needed to determine reasonable rotation steps, and the centre is needed to carry out a proper interpolation of the molecular transform. The extent and the centre are both given in Ångstroms.
- ENSEMBLE <MODLID> FRACTION <FRAC_SCAT>
- Fraction scattering of ensemble entered directly rather than calculated from composition
- ENSEMBLE <MODLID> BINS {MIN <L>} {MAX <H>} {NUM <N>} {WIDTH <W>} {CUBIC <A B C>}
- Bins for the MODLID
- ENSEMBLE <MODLID> DISABLE CHECK [ON|OFF]
- Toggle to disable checking of deviation between models in an ensemble. Use with extreme caution. Results of computations are not guaranteed to be sensible.
- Default: ENSEMBLE <MODLID> BINS MIN 5 MAX 200 WIDTH 1000 CUBIC 0 1 0
- Default: ENSEMBLE <MODLID> DISABLE CHECK OFF
HKLIN
- HKLIN <FILENAME>
- The mtz file containing the data
JOBS
- JOBS <NUM>
- Number of processors to use in parallelized sections of code
- Default: JOBS 2
LABIN
- LABIN F = <F> SIGF = <SIGF>
- Columns in mtz file. F must be given. SIGF should be given but is optional
MODE
- MODE [ ANO | CCA | NMA | NCS | MR_AUTO | MR_FRF | MR_FTF | MR_BRF | MR_BTF | MR_RNP | MR_LLG | MR_PAK | EP_AUTO | EP_SAD]
- The mode of operation of Phaser. The different modes are described in a separate page on Keyword Modes
PARTIAL
- PARTIAL PDB <PDBFILE> [RMS <RMS>|IDENTITY <ID>]
- The partial structure for SAD refinement
- PARTIAL HKLIN <MTZFILE> [RMS <RMS>|IDENTITY <ID>]
- The partial electron density for SAD refinement
SEARCH
- SEARCH ENSEMBLE <MODLID> {OR ENSEMBLE <MODLID>}… NUMBER <NUM>
- The ENSEMBLE to be searched for in a rotation search or an automatic search. When multiple ensembles are given using the OR keyword, the search is performed for each ENSEMBLE in turn. When the keyword is entered multiple times, each SEARCH keyword refers to a new component of the structure. If the component is present multiple times the sub-keyword NUMber can be used (rather than entering the same SEARCH keyword NUMber times).
- SEARCH ORDER AUTO [ON|OFF]
- Search in the "best" order as estimated using estimated rms deviation and completeness of models.
- SEARCH METHOD [FULL|FAST]
- Search using the "full search" or "fast search" algorithms.
- SEARCH DEEP [ON|OFF]
- Search method FAST only. Flag to control whether or not the cuttoff for the peaks in the rotation function is reduced if there is no TFZ over ZSCORE_CUTOFF in the first search.
- SEARCH DOWN PERCENT <PERC>
- Search method FAST only. Percentage to reduce rotation function cutoff if there is no TFZ over ZSCORE_CUTOFF in first search.
- SEARCH BFACTOR <BFAC>
- B-factor applied to search molecule (or atom).
- Default: SEARCH METHOD FAST
- Default: SEARCH ORDER AUTO ON
- Default: SEARCH DEEP ON
- Default: SEARCH DOWN PERCENT 25
- Default: SEARCH BFACTOR 0
SGALTERNATIVE
- SGALTERNATIVE SELECT [1ALL| 2HAND| 3LIST| 4NONE]
- Selection of alternative space groups to test in translation functions i.e. those that are in same laue group as that given in SPACEGROUP
- 1 Test all possible space groups,
- 2 Test the given space group and its enantiomorph.
- 3 Test the space groups listed with SGALTERNATIVE TEST <SG>.
- 4 Do not test alternative space groups.
- SGALTERNATIVE TEST <SG>
- Alternative space groups to test. Multiple test space groups can be entered.
- SGALTERNATIVE SORT [ON|OFF]
- Sort alternative space group list in order of frequency of occurrence.
- Default: SGALTERNATIVE SELECT HAND
- Default: SGALTERNATIVE SORT ON
SOLUTION
- SOLUTION SET <ANNOTATION>
- Start new set of solutions
- SOLUTION TEMPLATE
- Specifies a template solution against which other solutions in this run will be compared. Given in place of SOLUTION SET. Template rotation and translations given by subsequent SOLUTION 6DIM cards as per SOLUTION SETS.
- SOLUTION 6DIM ENSEMBLE <MODLID> EULER <A B G> [ORTH|FRAC] <X Y Z> FIXR [ON|OFF] FIXT [ON|OFF] FIXB [ON|OFF] BFAC <BFAC> MULT <MULT>
- This keyword is repeated for each known position and orientation of an ENSEMBLE MODLID. A B G are the Euler angles and X Y Z are the translation elements, expressed either in orthogonal Angstroms (ORTH) or fractions of a cell edge (FRAC). The input ensemble is transformed by a rotation around the origin of the coordinate system, followed by a translation. BFAC default to 0, MULT (for multiplicity) defaults to 1.
- SOLUTION SPACEGROUP <SPACEGROUP>
- Space Group of the solution (if alternative spacegroups searched).
- SOLUTION ENSEMBLE <MODLID> VRMS <V1> <V2> ...
- Refined RMS variance terms for pdb files (or map) in ensemble MODLID. If given as part of a solution, these values overwrite the values used for input in the ENSEMBLE keyword (if refined).
- SOLUTION SOLPAR FSOL <FSOL>
- Solvent parameters for the solution (if refined).
- SOLUTION TRIAL ENSEMBLE <MODLID> EULER <A B G> {RFZ <RFZ>}
- Rotation List for translation function
- SOLUTION ORIGIN ENSEMBLE <MODLID>
- Create solution for ensemble MODLID at the origin
SPACEGROUP
- SPACEGROUP <SG>
- Space group may be altered from the one on the MTZ file to a space group in the same point group. The space group name or number can be given e.g. P 21 21 21 or 19. l.
- Default: Read from MTZ file
WAVELENGTH
- WAVELENGTH <LAMBDA>
- The wavelengh at which the SAD dataset was collected
setWAVE(float <LAMBDA>)
Output Control Keywords
DEBUG
- DEBUG [ON|OFF]
- Extra verbose output for debugging
- Default: DEBUG OFF
setDEBU(bool <True=ON False=OFF>)
EIGEN
- EIGEN [ READ <EIGENFILE> | WRITE [ON|OFF] ]
- Read or write a file containing the eigenvectors and eigenvalues. If reading, the eigenvalues and eigenvectors of the atomic Hessian are read from the file generated by a previous run, rather than calculated. This option must be used with the job that generated the eigenfile and the job reading the eigenfile must have identical (or default) input for keyword NMAMethod. Use WRITe to control whether or not the eigenfile is written when not using the READ mode.
- Default: EIGEN WRITE ON
setEIGE_WRIT(bool <True=ON False=OFF>) setEIGE_READ(bool <True=ON False=OFF>)
HKLOUT
- HKLOUT [ON|OFF]
- Flags for output of an mtz file containing the phasing information
- Default: HKLOUT ON
setHKLO(bool <True=ON False=OFF>)
KEYWORDS
- KEYWORDS [ON|OFF]
- Write output Phaser .sol file (.rlist file for rotation function)
- Default: KEYWORDS ON
setKEYW(bool <True=ON False=OFF>)
MUTE
- MUTE [ON|OFF]
- Toggle for running in silent/mute mode, where no logfile is written to standard output.
- Default: MUTE OFF
setMUTE(bool <True=ON False=OFF>)
TITLE
- TITLE <TITLE>
- Title for job
- Default: TITLE [no title given]
setTITL(string <TITLE>)
TOPFILES
- TOPFILES <NUM>
- Number of top pdbfiles or mtzfiles to write to output.
- Default: TOPFILES 1
setTOPF(int <NUM>)
ROOT
- ROOT <FILEROOT>
- Root filename for output files (e.g. FILEROOT.log)
- Default: ROOT PHASER
setROOT(string <FILEROOT>)
VERBOSE
- VERBOSE [ON|OFF]
- Toggle to send verbose output to log file.
- Default: VERBOSE OFF
setVERB(bool <True=ON False=OFF>)
XYZOUT
- XYZOUT [ON|OFF] ENSEMBLE [ON|OFF]
- Toggle for output coordinate files. If the optional ENSEMBLE keyword is ON, then each placed ensemble is written to its own pdb file. The files are named FILEROOT.#.#.pdb with the first # being the solution number and the second # being the number of the placed ensemble (representing a SOLU 6DIM entry in the .sol file).
- Default: XYZOUT OFF (Rotation functions)
- Default: XYZOUT ON ENSEMBLE OFF (all other relevant modes)
setXYZO(bool <True=ON False=OFF>)
Advanced Keywords
ELLG
- ELLG USE [ON|OFF]
- Use expected LLG to determine resolution limits and search order
- ELLG TARGET <TARGET>
- Target value for expected LLG for determining resolution limits and search order
- Default: ELLG USE ON
- Default: ELLG TARGET 120
HAND
- HAND [ON|OFF|BOTH]
- Toggle for whether or not to use other hand of space group, or both hands, in experimental phasing
- Default: HAND BOTH
LLGCOMPLETE
- LLGComplete COMPLETE [ON|OFF]
- Toggle for structure completion by log-likelihood gradient maps
- LLGComplete SCATTERER <TYPE>
- Atom/Cluster type(s) to be used for log-likelihood gradient completion. If more than one element is entered for log-likelihood gradient completion, the atom type that gives the highest Z-score for each peak is selected. Type = "RX" is a purely real scatterer and type="AX" is purely anomalous scatterer
- LLGComplete CLASH <CLASH>
- Minimum distance between atoms in log-likelihood gradient maps and also the distance used for determining anisotropy of atoms (default determined by resolution, flagged by CLASH=0)
- LLGComplete SIGMA <Z>
- Z-score (sigma) for accepting peaks as new atoms in log-likelihood gradient maps
- LLGComplete NCYC <NMAX>
- Maximum number of cycles of log-likelihood gradient structure completion. By default, NMAX is 50, but this limit should never be reached, because all features in the log-likelihood gradient maps should be assigned well before 50 cycles are finished. This keyword should be used to reduce the number of cycles to 1 or 2.
- LLGComplete MAPS [ON|OFF]
- Output map coefficients to mtz file
- LLGComplete METHOD [IMAGINARY|ATOMTYPE]
- Pick peaks from the imaginary map only or from all the completion atomtype maps.
- Default: LLGCOMPLETE COMPLETE OFF
- Default: LLGCOMPLETE CLASH 0
- Default: LLGCOMPLETE SIGMA 6
- Default: LLGComplete NCYC 50
- Default: LLGComplete MAPS OFF
- Default: LLGComplete METHOD ATOMTYPE
NMAPDB
- NMAPDB PERTURB [RMS| DQ]
- Perturb the structure by rms devitations along the modes, or by set dq increments
- NMAPDB MODE <M1> {MODE <M2>…}
- The MODE keyword gives the mode along which to perturb the structure. If multiple modes are entered, the structure is perturbed along all the modes AND combinations of the modes given. There is no limit on the number of modes that can be entered, but the number of pdb files explodes combinatorially.
- NMAPDB COMBination <NMAX>
- Controls how many modes are present in any combination.
- NMAPDB RMS STEP <RMS>
- Increment in rms Ångstroms between pdb files to be written.
- NMAPDB RMS CLASH <CLASH>
- NMAPDB RMS STRETCH <STRETCH>
- NMAPDB RMS MAX <MAXRMS>
- The structure will be perturbed along each mode until either the C-alpha atoms clash with (come within CLASH Ångstroms of) other C-alpha atoms, the distances between C-alpha atoms STRETCH too far (note that normal modes do not preserve the geometry) or the MAXRMS deviation has been reached.
- NMAPDB RMS DIRECTION [FORWard|BACKward|TOFRo]
- The structure is perturbed either forwards or backwards or to-and-fro (FORWARD|BACKWARD|TOFRO) along the eigenvectors of the modes specified.
- NMAPDB DQ <DQ1> {DQ <DQ2>…}
- Alternatively, the DQ factors (as used by the Elnemo server (K. Suhre & Y-H. Sanejouand, NAR 2004 vol 32) ) by which to perturb the atoms along the eigenvectors can be entered directly.
- Default: NMAPDB MODE 7
- Default: NMAPDB COMBINATION 3
- Default: NMAPDB PERTURB RMS
- Default: NMAPDB RMS STEP 0.3
- Default: NMAPDB RMS STRETCH 5.0
- Default: NMAPDB RMS CLASH 2.0
- Default: NMAPDB RMS MAXRMS 0.5
- Default: NMAPDB RMS DIRECTION TOFRO
PACK
- PACK SELECT [ 1BEST | 2ALLOW | 3PERCENT | 4ALL ]
- 1Allow the best packing solutions only, provided the total number of clashes does not exceed ALLOWED_CLASHES
- 2Allow all solutions that pack with number of C-alpha clashes less than ALLOWED_CLASHES
- 3Allow up to the ALLOWED_CLASHES percentage of C-alpha atoms of the model structure to clash
- 4Allow all solutions (no packing test)
- If the model is RNA or DNA, phosphate (P) and carbon atoms (C3* and C4*) in the phosphate backbone, and nitrogen atoms in the bases are taken as the marker atoms for clashes. The atom names must start in column 14 (leaving one space at the beginning of the field), and the residue names must be right-justified (i.e. in column 20 for the single-letter names of ribonucleotides such as A, or in columns 19-20 for the two letter names of deoxyribonucleotides such as DA).
- PACK CUTOFF <ALLOWED_CLASHES>
- Limit on total number of clashes
- PACK QUICK [ON|OFF]
- Packing check stops when ALLOWED_CLASHES or MAX_CLASHES is reached. However, all clashes are found when the solution has a high Z-score (ZSCORE keyword).
- PACK DISTANCE <CLASH_DISTANCE>
- Distance within which C-alpha atoms clash given by CLASH_DISTANCE Ångstroms. If the model is RNA or DNA, phosphate and carbon atoms in the phosphate backbone, and nitrogen atoms in the bases are taken as the marker atoms for clashes
- PACK COMPACT [ON|OFF]
- Pack ensembles into a compact association (minimize distances between centres of mass for the addition of each component in a solution).
- PACK TRACE [ON|OFF]
- Toggle whether or not to only use Trace atoms (C-alpha atoms in proteins and P in RNA/DNA) for packing analysis, or all atoms. Only recommended to be OFF for use with small fragments.
- Default: PACK SELECT PERCENT
- Default: PACK CUTOFF 5
- Default: PACK QUICK ON
- Default: PACK DISTANCE 3.0
- Default: PACK COMPACT ON
- Default: PACK TRACE ON
PEAKS
- PEAKS [ROT|TRA] SELECT [ 1PERCENT | 2SIGMA | 3NUMBER | 4ALL] CUTOFF <CUTOFF>
- Peaks for the rotation function (ROT) or translation function (TRA) satisfying selection criteria are saved
- 1 Select peaks by taking all peaks over CUTOFF percent of the difference between the top peak and the mean value.
- 2 Select peaks by taking all peaks with a Z-score greater than CUTOFF.
- 3 Select peaks by taking top CUTOFF.
- 4 Select all peaks.
- PEAKS CUTOFF <CUTOFF>
- Cutoff value for peak selection criteria.
- PEAKS [ROT|TRA] CLUSTER [ON|OFF]
- Toggle for CLUSTER selects clustered peaks.
- Default: PEAKS ROT SELECT PERCENT
- Default: PEAKS TRA SELECT PERCENT
- Default: PEAKS ROT CUTOFF 75
- Default: PEAKS TRA CUTOFF 75
- Default: PEAKS ROT CLUSTER ON
- Default: PEAKS TRA CLUSTER ON
PERMUTATIONS
- PERMUTATIONS [ON|OFF]
- Only relevant to SEARCH MEHOD FULL. Toggle for whether the order of the search set is to be permuted.
- Default: PERMUTATIONS OFF
PURGE
- PURGE [ROT|TRA] ENABLE [ON|OFF]
- Toggle for whether to purge the solution list from the RF or TF and after the refinement steps (in AUTO mode) according to the best solution found so far.
- PURGE [ROT|TRA] PERCENT <PERC>
- PERC is the percent of the difference between the top solution and the mean at which to purge the solutions.
- PURGE [ROT|TRA] NUMBER <NUM>
- NUM is the number of solutions to retain in purging. The number taken is the minimum of the number found with the PERCENT cutoff and the NUMBER cutoff. Zero is flag to not use this criteria
- Default: PURGE ROT ENABLE ON PERC 75 NUM 0
- Default: PURGE TRA ENABLE ON PERC 75 NUM 0
RESOLUTION
- RESOLUTION HIGH <HIRES>
- High resolution limit in Ångstroms.
- RESOLUTION LOW <LORES>
- Low resolution limit in Ångstroms.
- RESOLUTION AUTO HIGH <HIRES>
- High resolution limit in Ångstroms for final high resolution refinement in MR_AUTO mode.
- RESOLUTION AUTO LOW <LORES>
- Low resolution limit in Ångstroms for final high resolution refinement in MR_AUTO mode.
- Default for molecular replacement: Set by ELLG TARGET for structure solution, final refinement uses all data
- Default for experimental phasing: All data used
ROTATE
- ROTATE VOLUME FULL
- Sample all unique angles
- ROTATE VOLUME AROUND EULER <A B G> RANGE <RANGE>
- Restrict the search to the region of +/- RANGE degrees around orientation given by EULER
- Constraint: RANGE>0
- Default: ROTATE VOLUME FULL
SCATTERING
- SCATTERING TYPE <TYPE> FP=<FP> FDP=<FDP> FIX [ON|OFF|EDGE]
- Measured scattering factors for a given atom type, from a fluorescence scan. FIX EDGE (default) fixes the fdp value if it is away from an edge, but refines it if it is close to an edge, while FIX ON or FIX OFF does not depend on proximity of edge.
- SCATTERING RESTRAINT [ON|OFF]
- use Fdp restraints
- SCATTERING SIGMA <SIGMA>
- Fdp restraint sigma used is SIGMA multiplied by initial fdp value
- Default: SCATTERING SIGMA 0.2
- Default: SCATTERING RESTRAINT ON
TNCS
- TNCS USE [ON|OFF]
- Use TNCS if present: apply TNCS corrections. (Note: was TNCS IGNORE [ON|OFF] in Phaser-2.4.0)
- TNCS REFINE ROTATION [ON | OFF]
- Use TNCS correction method that includes a rotation refinement of the two TNCS related rotations (to separate the rotation function results) before the translation function
- TNCS ROTATION ANGLE <rotx roty rotz>
- Input rotational difference between molecules related by the pseudo-translational symmetry vector, specified as rotations in degrees about x, y and z axes (GRID OFF). Central value for grid search (GRID ON).
- TNCS ROTATION GRID [ON | OFF]
- Refine the initial rotation angle starting from a grid of orientations around the starting angle (default 0,0,0). Grid controlled by RANGE and SAMPLING. The best refined rotational angle will be selected.
- TNCS ROTATION RANGE <angle>
- Maximum deviation from initial rotation from which to look for rotational deviation. Value of 0 means use internally determined defaultvalue based on resolution of data and size of G-function effective molecular radius.
- TNCS ROTATION SAMPLING <sampling>
- Sampling for rotation search. Value of 0 means use internally determined defaultvalue based on resolution of data and size of G-function effective molecular radius.
- TNCS TRA VECTOR <x y z>
- Input pseudo-translational symmetry vector (fractional coordinates). By default the translation is determined from the Patterson.
- TNCS VARIANCE RMSD <num>
- Input estimated rms deviation between pseudo-translational symmetry vector related molecules.
- TNCS VARIANCE FRAC <num>
- Input estimated fraction of cell content that obeys pseudo-translational symmetry.
- TNCS LINK RESTRAINT [ON | OFF]
- Link the occupancy of atoms related by TNCS in SAD phasing
- TNCS LINK SIGMA <sigma>
- Sigma of link restraint of the occupancy of atoms related by TNCS in SAD phasing
- TNCS PATT HIRES <hires>
- High resolution limit for Patterson calculation for TNCS detection
- TNCS PATT LORES <lores>
- Low resolution limit for Patterson calculation for TNCS detection
- TNCS PATT PERCENT <percent>
- Percent of origin Patterson peak that qualifies as a TNCS vector
- TNCS PATT DISTANCE <distance>
- Minium distance of Patterson peak from origin that qualifies as a TNCS vector
- TNCS NMOL <NMOL>
- Number of molecules/molecular assemblies related by single TNCS vector (usually only 2). If the TNCS is a pseudo-tripling of the cell then NMOL=3, a pseudo-quadrupling then NMOL=4 etc.
- Default: TNCS USE ON
- Default: TNCS REFINE ROTATION OFF
- Default: TNCS ROTATION ANGLE 0 0 0
- Default: TNCS ROTATION GRID ON
- Default: TNCS ROTATION SAMPLING 0
- Default: TNCS ROTATION RANGE 0
- Default: TNCS VARIANCE RMS 0.4
- Default: TNCS VARIANCE FRAC 1
- Default: TNCS LINK RESTRAINT ON
- Default: TNCS LINK SIGMA 0.1
- Default: TNCS PATT HIRES 5
- Default: TNCS PATT LORES 10
- Default: TNCS PATT PERCENT 20
- Default: TNCS PATT DISTANCE 15
- Default: TNCS NMOL 2
TRANSLATE
- TRANSLATE VOLUME FULL
- Search volume for brute force translation function. Cheshire cell or Primitive cell volume.
- TRANSLATE VOLUME LINE [ORTH|FRAC] START <XS YS ZS> END <XE YE ZE>
- Search volume for brute force translation function. Search along line.
- TRANSLATE VOLUME REGION [ORTH|FRAC] START <XS YS ZS> END <XE YE ZE>
- Search volume for brute force translation function. Search region.
- TRANSLATE VOLUME AROUND [ORTH|FRAC] POINT <X Y Z> RANGE <RANGE>
- Search volume for brute force translation function. Search within +/- RANGE Ångstroms (not fractional coordinates, even if the search point is given as fractional coordinates) of a point <X Y Z>.
- Default: TRANSLATE VOLUME FULL
ZSCORE
- ZSCORE USE [ON|OFF]
- Use the TFZ tests. Only applicable with SEARCH METHOD FAST. (Note Phaser-2.4.0 and below use "ZSCORE SOLVED 0" to turn off the TFZ tests)
- ZSCORE SOLVED <ZSCORE_SOLVED>
- Set the minimum TFZ that indicates a definite solution for amalgamating solutions in FAST search method.
- ZSCORE HALF [ON|OFF]
- Set the TFZ for amalgamating solutions in the FAST search method to the maximum of ZSCORE_SOLVED and half the maximum TFZ, to accommodate cases of partially correct solutions in very high TFZ cases (e.g. TFZ > 16)
- Default: ZSCORE USE ON
- Default: ZSCORE SOLVED 8
- Default: ZSCORE HALF ON
Expert Keywords
BOXSCALE
- BOXSCALE <BOXSCALE>
- Scale for box for calculating structure factors. The ensembles are put in a box equal to (extent of molecule)*BOXSCALE
- Default: BOXSCALE 4
MACANO
- MACANO PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]
- Protocol for the refinement of SigmaN in the anisotropy correction
- MACANO ANISOTROPIC [ON|OFF] BINS [ON|OFF] SOLK [ON|OFF] SOLB [ON|OFF] {NCYCle <NCYC>} {MINIMIZER [BFGS|NEWTON|DESCENT]}
- Macrocycle for the custom refinement of SigmaN in the anisotropy correction. Macrocycles are performed in the order in which they are entered.
- Default: MACANO PROTOCOL DEFAULT
MACMR
- MACMR PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]
- Protocol for refinement of molecular replacement solutions
- MACMR ROT [ON|OFF] TRA [ON|OFF] BFAC [ON|OFF] VRMS [ON|OFF] {NCYCLE <NCYC>} {MINIMIZER [BFGS|NEWTON|DESCENT]}
- Macrocycle for custom refinement of molecular replacement solutions. Macrocycles are performed in the order in which they are entered.
- Default: MACMR PROTOCOL DEFAULT
MACSAD
- MACSAD PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]
- Protocol for SAD refinement.
- n.b. PROTOCOL ALL will crash phaser and is only useful for debugging - see code for details
- MACSAD K [ON|OFF] B [ON|OFF] SIGMA [ON|OFF] XYZ [ON|OFF] OCCupancy [ON|OFF] BFACtor [ON|OFF] FDP [ON|OFF] SA [ON|OFF] SB [ON|OFF] SP [ON|OFF] SD [ON|OFF] {PK [ON|OFF]} {PB [ON|OFF]} {NCYCle <NCYC>} {MINIMIZER [BFGS|NEWTON|DESCENT]}
- Macrocycle for SAD refinement. Macrocycles are performed in the order in which they are entered.
- Default: MACSAD PROTOCOL DEFAULT
MACTNCS
- MACTNCS PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]
- Protocol for pseudo-translational NCS refinement.
- MACTNCS ROT [ON|OFF] TRA [ON|OFF] VRMS [ON|OFF] {SOLP [ON|OFF} {LAST [ON|OFF} {NCYCLE <NCYC>} {MINIMIZER [BFGS|NEWTON|DESCENT]}
- Macrocycle for pseudo-translational NCS refinement. Macrocycles are performed in the order in which they are entered.
- Default: MACTNCS PROTOCOL DEFAULT
NMAMETHOD
- NMAMETHOD OSCILLATORS [RTB | CA | ALL ]
- Define the atoms used for the normal mode analysis. RTB uses the rotation-translation block method, CA uses C-alpha atoms only to determine the modes, and ALL uses all atoms to determine the modes (only for use on very small molecules, less than 250 atoms).
- NMAMETHOD MAXBLOCKS <MAXBLOCKS>
- MAXBLOCKS is the number of rotation-translation blocks for the RTB analysis.
- NMAMETHOD NRES <NRES>
- For the RTB analysis, by default NRES=0 and then it is calculated so that it is as small as it can be without reaching MAXBlocks.
- NMAMETHOD RADIUS <RADIUS>
- Elastic Network Model interaction radius (Angstroms)
- NMAMETHOD FORCE <FORCE>
- Elastic Network Model force constant
- Default: NMAMETHOD OSCILLATORS RTB MAXBLOCKS 250 NRES 0 RADIUS 5 FORCE 1
RESCORE
- RESCORE [ROT|TRA] [ON|OFF]
- Toggle for rescoring of fast rotation function (ROT) or fast translation function (TRA) search peaks.
- Default: RESCORE ROT ON
- Default: RESCORE TRA ON|OFF will depend on whether phaser is running in the mode MODE MR_AUTO with search method SEARCH METHOD FAST or with SEARCH METHOD FULL, or running the translation function separately MODE MR_FTF. For SEARCH METHOD FAST the default also depends on whether or not the expected LLG target ELLG TARGET <TARGET> value is reached.
RESHARPEN
- RESHARPEN PERCENTAGE <PERC>
- Perecentage of the B-factor in the direction of lowest fall-off (in anisotropic data) to add back into the structure factors F_ISO and FWT and FDELWT so as to sharpen the electron density maps
- Default: RESHARPEN PERCENT 100
SAMPLING
- SAMPLING [ROT|TRA]
- Sampling of search given in degrees for a rotation search and Ångstroms for a translation search. Sampling for rotation search depends on the mean radius of the Ensemble and the high resolution limit (dmin) of the search.
- Default: SAMP = 2*atan(dmin/(4*meanRadius)) (MODE = MR_BRF or MR_FRF)
- Default: SAMP = dmin/5; (MODE = MR_BTF)
- Default: SAMP = dmin/4; (MODE = MR_FTF)
Developer Keywords
BINS
- BINS {MIN <L>} {MAX <H>} {WIDTH <W>} {CUBIC <A B C>}
- The binning of the data. L = minimum number of bins, H = maximum number of bins, W = width of the bins in number of reflections, A B C are the coefficients for the binning function A(S*S*S)+B(S*S)+CS where S = (1/resolution). If N is given then the values of L and H are ignored.
- Constraint: CUBIC coefficients restricted to monotonically increasing function: A >0, B >0, C >0 and either (a) A=B=0 or (b) A=0 or (c) B=0
- Default: BINS MIN 6 MAX 50 WIDTH 500 CUBIC 0 1 0
BFACTOR
- BFACTOR WILSON RESTRAINT [ON|OFF]
- Toggle to use the Wilson restraint on the isotropic component of the atomic B-factors in SAD phasing.
- BFACTOR SPHERICITY RESTRAINT [ON|OFF]
- Toggle to use the sphericity restraint on the anisotropic B-factors in SAD phasing
- BFACTOR REFINE RESTRAINT [ON|OFF]
- Toggle to use the restraint to zero for molecular Bfactor in molecular replacement.
- BFACTOR WILSON SIGMA <SIGMA>
- The sigma of the Wilson restraint.
- BFACTOR SPHERICITY SIGMA <SIGMA>
- The sigma of the sphericity restraint.
- BFACTOR REFINE SIGMA <SIGMA>
- The sigma of the sphericity restraint.
- Default: BFACTOR WILSON RESTRAINT ON
- Default: BFACTOR SPHERICITY RESTRAINT ON
- Default: BFACTOR REFINE RESTRAINT ON
- Default: BFACTOR WILSON SIGMA 5
- Default: BFACTOR SPHERICITY SIGMA 5
- Default: BFACTOR REFINE SIGMA 10
CELL
- CELL <A B C ALPHA BETA GAMMA>
- Unit cell dimensions
- Default: Cell read from MTZ file
CLMN
- CLMN SPHERE <SPHERE>
- Radius for the decomposition of the Patterson in Ångstroms. If it is 0, the radius defaults to twice the mean radius of the ENSEMBLE.
- CLMN LMIN <LMIN>
- Lower limit of L values.
- CLMN LMAX <LMAX>
- Upper limit of L values. The largest L value used in the calculation is the minimum of LMAX and 2π * SPHERE/dmin.
- Default: CLMN LMIN 4
- Default: CLMN LMAX 100
- Default: CLMN SPHE 0
FFTS
- FFTS MIN [ATOMS_MIN] MAX [ATOMS_MAX]
- The minimum and maximum number of atoms of the range between which direct summation and fft methods are tested to see which is faster for structure factor and gradient calcuation (for this unit cell and resolution). For a number of atoms below ATOMS_MIN direct structure factor calculation is always used, and for a number of atoms above ATOMS_MAX ffts are always used for the structure factor calculation and the gradient calculations. Direct summation is always used for the curvatures. Use FFTS MIN 0 MAX O to always use ffts.
- Default: FFTS MIN 20 MAX 80
INTEGRATION
- INTEGRATION FIXED [ON | OFF]
- Fix the number of integration points or determine the number of angular steps in the integration by the variance of the function
- INTEGRATION STEP <STEP>
- Number of steps in angular integration of function if FIXED number of points
- Default: INTEGRATION FIXED OFF
MACHL
- MACHL PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]
- Protocol for refinement of Hendrickson-Lattman coefficients
- MACHL COEFFICIENTS [ON|OFF] {NCYCle <NCYC>} {MINIMIZER [BFGS|NEWTON|DESCENT]}
- Macrocycle for custom refinement of Hendrickson-Lattman coefficients. Macrocycles are performed in the order in which they are entered.
- Default: MACHL PROTOCOL DEFAULT
NORMALIZATION
- NORMALIZATION BINS <B1 B2 ...> ANISO <HH KK LL HK HL KL> SOLK <SOLK> SOLB <SOLB>
- The normalization factors that correct for anisotropy in the data
OUTLIER
- OUTLIER REJECT [ON|OFF]
- Reject low probability data outliers
- OUTLIER PROB <PROB>
- Cutoff for rejection of low probablity outliers
- Default: OUTLIER REJECT ON PROB 0.000001
PTGROUP
- PTGROUP COVERAGE <COVERAGE>
- Percentage coverage for two sequences to be considered in same pointgroup
- PTGROUP IDENTITY <IDENTITY>
- Percentage identity for two sequences to be considered in same pointgroup
- PTGROUP RMSD <RMSD>
- Percentage rmsd for two models to be considered in same pointgroup
- PTGROUP TOLERANCE ANGULAR <ANG>
- Angular tolerance for pointgroup
- PTGROUP TOLERANCE SPATIAL <DIST>
- Spatial tolerance for pointgroup
SOLPARAMETERS
- SOLPARAMETERS FSOL <FSOL> BSOL <BSOL> FIXB [ON|OFF]
- Babinet solvent parameters for Sigma(A) curves. If FIXB is OFF, then BSOL is calculated from FSOL using the formula BSOL = 99.1 + 5.79*exp(4.03*FSOL) from Glykos & Kokkinkdis Acta Cryst D56 p1070 (2000), otherwise BSOL is fixed at the input (or default) value.
- SOLPARAMETERS RESTRAIN [ON|OFF]
- Restrain the Babinet solvent parameters to the initial values during refinement.
- SOLPARAMETERS RESOLUTION <HIRES>
- Do not apply Babinet solvent correction terms to resolutions higher than HIRES.
- Default: SOLPARAMETERS FSOL 0.69 BSOL 378 FIXB ON
- Default: SOLPARAMETERS RESTRAINT OFF
- Default: SOLPARAMETERS RESOLUTION 0
SORT
- SORT [ON|OFF]
- Sort the reflections into resolution order upon reading MTZ file, for performance gain in molecular replacement
- Default: SORT ON
TARGET
- TARGET FRF [LERF1|LERF2|CROWTHER]
- Target function for fast rotation searches (2)
- TARGET FTF [LETF1|LETF2|CORRELATION]
- Target function for fast translation searches (3)
- Default: TARGET FRF LERF1
- Default: TARGET FTF LETF1
VARSAD
- VARSAD [ K <N> | B <N> | SIGMA <N> | SA <B1 B2 …> | SB <B1 B2 …> | SP <B1 B2 …> | SD <B1 B2 …> | PK <N> | PB <N>]
- SAD variance parameters SA and SB (the real and imaginary components of Sigma Minus), SP (Sigma Plus) and SD (Sigma Delta) by resolution bin, the overall scale (K) and B-factor (B) for the anomalous scatterer model, the overall scale (PK) and B-factor (PB) for the partial structure (if given), and sigma-scale (SIGMA).